CRISPR Primer Designer： Design primers for knockout and chromosome imaging CRISPR-Cas system

• Published in: Journal of integrative plant biology Vol. 57; no. 7; pp. 613 - 617
• Main Authors: Yan, Meng, Zhou, Shi-Rong, Xue, Hong-Wei
• Format: Journal Article
• Language: English
• Published: China (Republic : 1949- ) Blackwell Publishing Ltd 01.07.2015; National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences,Shanghai 200032, China
• Subjects: biologists; Cas系统; Chromosome imaging; chromosomes; Chromosomes, Plant - genetics; Clustered Regularly Interspaced Short Palindromic Repeats - genetics; CRISPR; CRISPR-Cas Systems - genetics; DNA Primers - metabolism; epigenetics; Gene Knockout Techniques; genes; image analysis; Imaging, Three-Dimensional; Internet; knockout; plasmids; primer; researchers; Software; 基因敲除; 基因组结构; 多参数分析; 引物设计; 成像系统; 染色体; 设计工具; knockout; CRISPR; software; primer; Chromosome imaging
• ISSN: 1672-9072; 1744-7909; 1744-7909
• DOI: 10.1111/jipb.12295

The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR Primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system.